client: restore the previous name for the facet parameter, #TASK-7152…

…, #TASK-7134
opencb · Jan 16, 2025 · 9761058 · 9761058
1 parent 4f25cc8
commit 9761058
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Showing 49 changed files with 85 additions and 80 deletions.
diff --git a/...a-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java b/...a-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java
@@ -163,7 +163,7 @@ private RestResponse<FacetField> aggregationStats() throws Exception {
         queryParams.putIfNotEmpty("samples", commandOptions.samples);
         queryParams.putIfNotEmpty("numSamples", commandOptions.numSamples);
         queryParams.putIfNotEmpty("release", commandOptions.release);
-        queryParams.putIfNotEmpty("aggregationFields", commandOptions.aggregationFields);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }

diff --git a/...src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java b/...src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java
@@ -156,7 +156,7 @@ private RestResponse<FacetField> aggregationStats() throws Exception {
         queryParams.putIfNotEmpty("acl", commandOptions.acl);
         queryParams.putIfNotEmpty("release", commandOptions.release);
         queryParams.putIfNotNull("snapshot", commandOptions.snapshot);
-        queryParams.putIfNotEmpty("aggregationFields", commandOptions.aggregationFields);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }

diff --git a/...-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java b/...-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java
@@ -166,7 +166,7 @@ private RestResponse<FacetField> aggregationStats() throws Exception {
         queryParams.putIfNotEmpty("acl", commandOptions.acl);
         queryParams.putIfNotEmpty("release", commandOptions.release);
         queryParams.putIfNotNull("snapshot", commandOptions.snapshot);
-        queryParams.putIfNotEmpty("aggregationFields", commandOptions.aggregationFields);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }

diff --git a/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java b/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java
@@ -244,7 +244,7 @@ private RestResponse<FacetField> aggregationStats() throws Exception {
         queryParams.putIfNotEmpty("acl", commandOptions.acl);
         queryParams.putIfNotNull("deleted", commandOptions.deleted);
         queryParams.putIfNotEmpty("release", commandOptions.release);
-        queryParams.putIfNotEmpty("aggregationFields", commandOptions.aggregationFields);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }

diff --git a/...p/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java b/...p/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java
@@ -182,7 +182,7 @@ private RestResponse<FacetField> aggregationStats() throws Exception {
         queryParams.putIfNotEmpty("acl", commandOptions.acl);
         queryParams.putIfNotEmpty("release", commandOptions.release);
         queryParams.putIfNotNull("snapshot", commandOptions.snapshot);
-        queryParams.putIfNotEmpty("aggregationFields", commandOptions.aggregationFields);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java
@@ -176,7 +176,7 @@ private RestResponse<FacetField> aggregationStats() throws Exception {
         queryParams.putIfNotEmpty("acl", commandOptions.acl);
         queryParams.putIfNotEmpty("release", commandOptions.release);
         queryParams.putIfNotNull("deleted", commandOptions.deleted);
-        queryParams.putIfNotEmpty("aggregationFields", commandOptions.aggregationFields);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }

diff --git a/...a-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java b/...a-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java
@@ -195,7 +195,7 @@ private RestResponse<FacetField> aggregationStats() throws Exception {
         queryParams.putIfNotEmpty("statsBiotypeCount", commandOptions.statsBiotypeCount);
         queryParams.putIfNotEmpty("statsClinicalSignificanceCount", commandOptions.statsClinicalSignificanceCount);
         queryParams.putIfNotEmpty("statsConsequenceTypeCount", commandOptions.statsConsequenceTypeCount);
-        queryParams.putIfNotEmpty("aggregationFields", commandOptions.aggregationFields);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }

diff --git a/...src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java b/...src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
@@ -238,7 +238,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
         public boolean deleted = false; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }
@@ -596,7 +596,7 @@ public class AggregationStatsInterpretationCommandOptions {
         @Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
         public String release; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java
@@ -146,8 +146,8 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--release"}, description = "release", required = false, arity = 1)
         public String release; 
 
-        @Parameter(names = {"--aggregation-fields"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
-        public String aggregationFields; 
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        public String field; 
 
     }
 

diff --git a/...pp/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java b/...pp/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java
@@ -154,8 +154,8 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
         public Integer snapshot; 
 
-        @Parameter(names = {"--aggregation-fields"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
-        public String aggregationFields; 
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        public String field; 
 
     }
 

diff --git a/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java b/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java
@@ -162,8 +162,8 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
         public Integer snapshot; 
 
-        @Parameter(names = {"--aggregation-fields"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
-        public String aggregationFields; 
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        public String field; 
 
     }
 

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java
@@ -213,8 +213,8 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
         public String release; 
 
-        @Parameter(names = {"--aggregation-fields"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
-        public String aggregationFields; 
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        public String field; 
 
     }
 

diff --git a/...-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java b/...-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java
@@ -185,8 +185,8 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
         public Integer snapshot; 
 
-        @Parameter(names = {"--aggregation-fields"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
-        public String aggregationFields; 
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        public String field; 
 
     }
 

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java
@@ -158,8 +158,8 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
         public boolean deleted = false; 
 
-        @Parameter(names = {"--aggregation-fields"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
-        public String aggregationFields; 
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        public String field; 
 
     }
 

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java
@@ -227,8 +227,8 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--stats-consequence-type-count"}, description = "Sample variant stats ConsequenceTypeCount", required = false, arity = 1)
         public String statsConsequenceTypeCount; 
 
-        @Parameter(names = {"--aggregation-fields"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
-        public String aggregationFields; 
+        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        public String field; 
 
     }
 

diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R
@@ -107,7 +107,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinic
         #' @param internalStatus Filter by internal status.
         #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
         #' @param deleted Boolean to retrieve deleted entries.
-        #' @param field List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1.
+        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),
@@ -194,7 +194,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinic
         #' @param status Filter by status.
         #' @param internalStatus Filter by internal status.
         #' @param release Release when it was created.
-        #' @param field List of fields separated by semicolons, e.g.: studies;type;numSamples[0..10]:1.
+        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStatsInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
                 subcategory="clinical/interpretation", subcategoryId=NULL, action="aggregationStats", params=params,
                 httpMethod="GET", as.queryParam=NULL, ...),

diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R
@@ -20,7 +20,7 @@
 #' | endpointName | Endpoint WS | parameters accepted |
 #' | -- | :-- | --: |
 #' | updateAcl | /{apiVersion}/cohorts/acl/{members}/update | study, members[*], action[*], body[*] |
-#' | aggregationStats | /{apiVersion}/cohorts/aggregationStats | study, id, name, uuid, type, creationDate, modificationDate, deleted, status, internalStatus, annotation, acl, samples, numSamples, release, aggregationFields |
+#' | aggregationStats | /{apiVersion}/cohorts/aggregationStats | study, id, name, uuid, type, creationDate, modificationDate, deleted, status, internalStatus, annotation, acl, samples, numSamples, release, field |
 #' | loadAnnotationSets | /{apiVersion}/cohorts/annotationSets/load | study, variableSetId[*], path[*], parents, annotationSetId, body |
 #' | create | /{apiVersion}/cohorts/create | include, exclude, study, variableSet, variable, includeResult, body[*] |
 #' | distinct | /{apiVersion}/cohorts/distinct | study, id, name, uuid, type, creationDate, modificationDate, deleted, status, internalStatus, annotation, acl, samples, numSamples, release, field[*] |
@@ -68,7 +68,7 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort,
         #' @param samples Cohort sample IDs.
         #' @param numSamples Number of samples.
         #' @param release release.
-        #' @param aggregationFields List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="cohorts", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R
@@ -20,7 +20,7 @@
 #' | endpointName | Endpoint WS | parameters accepted |
 #' | -- | :-- | --: |
 #' | updateAcl | /{apiVersion}/families/acl/{members}/update | study, members[*], action[*], propagate, body[*] |
-#' | aggregationStats | /{apiVersion}/families/aggregationStats | study, id, name, uuid, members, expectedSize, samples, phenotypes, disorders, creationDate, modificationDate, deleted, internalStatus, status, annotation, acl, release, snapshot, aggregationFields |
+#' | aggregationStats | /{apiVersion}/families/aggregationStats | study, id, name, uuid, members, expectedSize, samples, phenotypes, disorders, creationDate, modificationDate, deleted, internalStatus, status, annotation, acl, release, snapshot, field |
 #' | loadAnnotationSets | /{apiVersion}/families/annotationSets/load | study, variableSetId[*], path[*], parents, annotationSetId, body |
 #' | create | /{apiVersion}/families/create | include, exclude, study, members, includeResult, body[*] |
 #' | distinct | /{apiVersion}/families/distinct | study, id, name, uuid, members, expectedSize, samples, phenotypes, disorders, creationDate, modificationDate, deleted, internalStatus, status, annotation, acl, release, snapshot, field[*] |
@@ -71,7 +71,7 @@ setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, families
         #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
         #' @param release Release when it was created.
         #' @param snapshot Snapshot value (Latest version of the entry in the specified release).
-        #' @param aggregationFields List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="families", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R
@@ -20,7 +20,7 @@
 #' | endpointName | Endpoint WS | parameters accepted |
 #' | -- | :-- | --: |
 #' | updateAcl | /{apiVersion}/files/acl/{members}/update | study, members[*], action[*], body[*] |
-#' | aggregationStats | /{apiVersion}/files/aggregationStats | study, id, uuid, name, path, uri, type, bioformat, format, external, status, internalStatus, internalVariantIndexStatus, softwareName, directory, creationDate, modificationDate, description, tags, size, sampleIds, jobId, annotation, acl, deleted, release, aggregationFields |
+#' | aggregationStats | /{apiVersion}/files/aggregationStats | study, id, uuid, name, path, uri, type, bioformat, format, external, status, internalStatus, internalVariantIndexStatus, softwareName, directory, creationDate, modificationDate, description, tags, size, sampleIds, jobId, annotation, acl, deleted, release, field |
 #' | loadAnnotationSets | /{apiVersion}/files/annotationSets/load | study, variableSetId[*], path[*], parents, annotationSetId, body |
 #' | bioformats | /{apiVersion}/files/bioformats |  |
 #' | create | /{apiVersion}/files/create | study, parents, body[*] |
@@ -95,7 +95,7 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, file, file
         #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
         #' @param deleted Boolean to retrieve deleted entries.
         #' @param release Release when it was created.
-        #' @param aggregationFields List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="files", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),